rs7550106

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000593011.5(FLG-AS1):​n.296+56306T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,080 control chromosomes in the GnomAD database, including 37,181 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.67 ( 37181 hom., cov: 32)

Consequence

FLG-AS1
ENST00000593011.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.364
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FLG-AS1NR_186761.1 linkuse as main transcriptn.354-24169T>C intron_variant
FLG-AS1NR_186762.1 linkuse as main transcriptn.179+35245T>C intron_variant
FLG-AS1NR_186763.1 linkuse as main transcriptn.206+35218T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FLG-AS1ENST00000420707.5 linkuse as main transcriptn.159-24169T>C intron_variant 5
FLG-AS1ENST00000593011.5 linkuse as main transcriptn.296+56306T>C intron_variant 4
FLG-AS1ENST00000630125.3 linkuse as main transcriptn.179+35245T>C intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.674
AC:
102492
AN:
151962
Hom.:
37159
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.441
Gnomad AMI
AF:
0.804
Gnomad AMR
AF:
0.597
Gnomad ASJ
AF:
0.680
Gnomad EAS
AF:
0.372
Gnomad SAS
AF:
0.561
Gnomad FIN
AF:
0.816
Gnomad MID
AF:
0.715
Gnomad NFE
AF:
0.840
Gnomad OTH
AF:
0.681
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.674
AC:
102541
AN:
152080
Hom.:
37181
Cov.:
32
AF XY:
0.667
AC XY:
49604
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.441
Gnomad4 AMR
AF:
0.597
Gnomad4 ASJ
AF:
0.680
Gnomad4 EAS
AF:
0.373
Gnomad4 SAS
AF:
0.563
Gnomad4 FIN
AF:
0.816
Gnomad4 NFE
AF:
0.840
Gnomad4 OTH
AF:
0.685
Alfa
AF:
0.741
Hom.:
7392
Bravo
AF:
0.649
Asia WGS
AF:
0.439
AC:
1528
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
5.7
DANN
Benign
0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7550106; hg19: chr1-152197202; API